Gradients in nucleotide and codon usage along Escherichia coli genes

Area of Science:

• Genomics and Molecular Biology
• Bioinformatics
• Evolutionary Biology

Background:

• Nucleotide and codon usage patterns exhibit systematic variations along gene sequences, forming usage gradients.
• These gradients can be influenced by both mutational pressures and selective forces, particularly related to gene expression and translation.
• Understanding these variations in model organisms like Escherichia coli provides insights into fundamental biological processes.

Purpose of the Study:

• To investigate the gradients of nucleotide and nucleotide combination usage within Escherichia coli genes.
• To differentiate between mutational and selectional effects on these usage patterns by analyzing genes with varying codon bias.
• To identify specific nucleotide combinations and their positional preferences that correlate with translational efficiency and error propensity.

Main Methods:

• Genes in Escherichia coli were categorized into three groups based on distinct codon usage bias.
• Analysis focused on the gradients of nucleotide and nucleotide combination usage along the gene sequences within each group.
• Investigated the immediate sequence context surrounding specific nucleotides to understand positional effects.

Main Results:

• Identified nucleotide combinations associated with translational processivity errors exhibiting strong negative usage gradients.
• Observed that these negative gradients weaken in genes with lower codon usage bias, suggesting selection plays a role.
• Detected a pervasive positive gradient for guanine (G) at the third codon position across most surrounding base contexts.

Conclusions:

• The observed gradients, particularly the weakening of negative gradients for error-prone combinations in low-bias genes, support the hypothesis of selection for translational efficiency.
• The pervasive positive gradient for third-position guanine indicates a significant, context-dependent selection pressure or mutational bias.
• This study highlights the complex interplay of mutation and selection in shaping nucleotide usage patterns and gene properties within a bacterial genome.